cAb-Rep: A Database of Curated Antibody Repertoires for Exploring Antibody Diversity and Predicting Antibody Prevalence

Front Immunol. 2019 Oct 9;10:2365. doi: 10.3389/fimmu.2019.02365. eCollection 2019.

Abstract

The diversity of B cell receptors provides a basis for recognizing numerous pathogens. Antibody repertoire sequencing has revealed relationships between B cell receptor sequences, their diversity, and their function in infection, vaccination, and disease. However, many repertoire datasets have been deposited without annotation or quality control, limiting their utility. To accelerate investigations of B cell immunoglobulin sequence repertoires and to facilitate development of algorithms for their analysis, we constructed a comprehensive public database of curated human B cell immunoglobulin sequence repertoires, cAb-Rep (https://cab-rep.c2b2.columbia.edu), which currently includes 306 immunoglobulin repertoires from 121 human donors, who were healthy, vaccinated, or had autoimmune disease. The database contains a total of 267.9 million V(D)J heavy chain and 72.9 million VJ light chain transcripts. These transcripts are full-length or near full-length, have been annotated with gene origin, antibody isotype, somatic hypermutations, and other biological characteristics, and are stored in FASTA format to facilitate their direct use by most current repertoire-analysis programs. We describe a website to search cAb-Rep for similar antibodies along with methods for analysis of the prevalence of antibodies with specific genetic signatures, for estimation of reproducibility of somatic hypermutation patterns of interest, and for delineating frequencies of somatically introduced N-glycosylation. cAb-Rep should be useful for investigating attributes of B cell sequence repertoires, for understanding characteristics of affinity maturation, and for identifying potential barriers to the elicitation of effective neutralizing antibodies in infection or by vaccination.

Keywords: B cell response; antibody prevalence; antibody repertoire; antibodyomics; gene-specific substitution profile; next-generation sequencing; post-translational modification; somatic hypermutation (SHM).

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Antibody Diversity*
  • Autoimmune Diseases / genetics
  • Autoimmune Diseases / immunology
  • Databases, Nucleic Acid*
  • Humans
  • Immunoglobulin Heavy Chains / genetics*
  • Infections / genetics
  • Infections / immunology
  • Vaccination

Substances

  • Immunoglobulin Heavy Chains